Open flangelier opened 9 years ago
Have you try reducing the executor and driver memory in Spark? See: https://github.com/GELOG/adamcloud/issues/11#issuecomment-85769275
How did you generate SRR062634.adam?
If order, you have to :
mkdir -p /data/ wget -O /data/chr1.fa.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz gzip -d /data/chr1.fa.gz
docker run --rm=true -ti -v /data:/data gelog/snap index /data/chr1.fa /data/snap-index.chr1
wget -O /data/SRR062634.filt.fastq.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/sequence_read/SRR062634.filt.fastq.gz gzip -d /data/SRR062634.filt.fastq.gz
docker run --rm=true -ti -v /data:/data gelog/snap single /data/snap-index.chr1/ /data/SRR062634.filt.fastq -o /data/SRR062634.sam
docker run --rm=true -ti -v /data/:/data gelog/adam adam-submit transform /data/SRR062634.sam /data/SRR062634.adam
You should now have all the needed files
The file SRR062634.filt.fastq.gz file contains the bogus reads that have been filtered out after quality control.
Try to feed this file to ADAM: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
Error:
docker run -ti --rm --name client-genomics -v /data:/data gelog/avocado /bin/bash avocado-submit /data/SRR062634.adam /data/chr1.fa /data/SRR062634.avr /usr/local/avocado/avocado-sample-configs/basic.properties
You can get the files by following the step from :